Serebella

See also:

• Science: Biology: Flora and Fauna  (22,696)
• Science: Biology: Genetics  (1,029)
• Science: Environment: Biodiversity  (948)

• American Society of Plant Taxonomists - Promotes research and teaching in the taxonomy, systematics, and phylogeny of vascular and nonvascular plants.
• Biomedical Ontology - About two dozen links collected by the Ontology Project at the philosophy department of State University of New York at Buffalo.
• BioNET - International - A global network of country-owned collaborative LOOPs to support national programs for biosystematics to support goals in areas such as sustainable development and pest management.
• Curiosities of Biological Nomenclature - Etymologies, puns and funny sounds and wordplay in taxonomy.
• DELTA: Description Language for Taxonomy - A flexible format for encoding taxonomic descriptions for computer processing. It can be used to produce natural-language descriptions, conventional or interactive keys, classifications, and information-retrieval systems.
• ETI World Taxonomist Database - Directory of specialists searchable by name, country, or specialization.
• European Consortium for the Barcode of Life - Project for DNA barcoding from a European perspective. List of European research institutes and researchers involved. Importance of DNA barcoding for taxonomy, the science of categorizing life forms.
• Expert Center for Taxonomic Identification - ETI is a non-governmental organisation in operational relations with UNESCO. Their mission is to develop scientific/educational computer-aided information systems, to improve general access to, and to promote use of taxonomic and biodiversity knowledge worldwide.
• Fairchild Tropical Garden Virtual Herbarium - Includes photos of more than 50,000 plant, palm, cycad and other cultivated tropical plants from Florida and taxonomic information on grasses, especially bamboos, and other economically important and interesting plants.
• Glossary of Phylogenetic Systematics - An annotated, extensive hypertext glossary of the terminology of Phylogenetic Systematics, with a discussion and criticism of mainstream Computer Cladistics.
• Integrated Taxonomic Information System - Authoritative taxonomic information on plants, animals, fungi, and microbes of North America and the world.
• Is it Time to Revise the System of Scientific Naming? - Article from National Geographic News arguing that the taxonomic classification system devised by Linnaeus is outdated by genetic research that shows that morphological similarities are not necessarily proof of evolutionary relatedness.
• Learn Plants Now - Strategies and tips for learning how to identify plants in the field. Introduction to botanical terms, checklist for plant identification, recommended resources.
• NCBI Taxonomy Homepage - Provides a taxonomy browser, taxonomy resources and other information.
• Partnerships for Enhancing Expertise in Taxonomy - National Science Foundation (USA) competition to support competitively reviewed research projects that target groups of poorly known organisms.
• Pickett Lab: Taxonomy, Evolution and Behavior - Dr Kurt M. Pickett is leading research into the taxonomy of the Vespidae, the role of taxonomy in biology and various methodological and computational issues in phylogenetics.
• Project Linnaeus - Ambitious project to classify all forms of life that exist on the planet Earth and catalog the information about them for conservation and research purposes and the pursuit of knowledge.
• Scalenet - Glossary - A short glossary explaining some of the terms used in taxonomy. From a site on scale insects.
• Science at the Natural History Museum - A world leader for research on taxonomy and biodiversity.
• ScientificName.net - Searchable database providing scientific names for many plants and animals.
• Systema Naturae 2000 - An up-to-date historical cross-referenced classification of life based on original authoritative scientific literature.
• Taxonomy - Information from Wikipedia on the practice and science of classification, the arrangement of organisms in a hierarchical structure.
• Taxonomy and Systematics at Glasgow - About taxonomy and systematics at the University of Glasgow, with links to other internet resources on these subjects.
• Tree of Life - A project containing information about the diversity of organisms on Earth, their history, and characteristics. The information is linked together in the form of the evolutionary tree that connects all organisms to each other.
• Treebase - A relational database of phylogenetic trees and the data matrices used to generate them from published research papers. Includes animals, plants, and fungi.
• Universal Biological Indexer and Organizer - A networked information service for biological information resources, based upon the Taxonomic Name Server, a thesaurus of taxonomic information.

Serebella

See also:

• Science: Biology: Evolution: Software  (11)
• Science: Biology: Software  (29)
• Science: Earth Sciences: Paleontology: Products and Services: Software  (3)
• Science: Math: Statistics: Software  (177)

• PAUP*   - PAUP is the most widely used package for phylogenetic inference, and now implements maximum likelihood and distance methods as well as various forms of parsimony. Powerful and very easy to use, particularly the Mac version.
• PHYLIP   - Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, likelihood and parsimony methods for a wide range of different types of data, and runs on most platforms.

• Clann: Software for Supertree Methods - Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees.
• Component - For analysis of phylogenies. Includes a wide range of randomization methods, consensus methods, tree comparison measures, and calculates reconciled trees. Now aging, and available only for Windows machines, but still has some unique features. Much of the functionality is now replaced by RadCon, GeneTree, TreeMap and the latest release of PAUP.
• GeneTree - Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the phylogenies by postulating horizontal transfer, gene duplication and loss events. Reprints of papers describing the methods are available from the GeneTree web page. Available for Macintosh and Windows.
• 3I - Internet-accessible Interactive Identification - Program to create internet-accessible interactive taxonomic keys.
• MacClade - A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer phylogeny, but excels in studying character evolution. Also provides tools for entering and editing data and phylogenies and producing attractive tree diagrams and charts.
• Mesquite - Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
• MrBayes - Open source software for estimation of phylogenies using Bayesian inference.
• NONA - Freeware software for phylogenetic analyses using parsimony.
• NONA - A Quick Guide to the Commands - A brief overview of using NONA for phylogenetic analysis.
• PAML - Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
• Phylodendron - Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform.
• Phylo-Win - Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
• r8s - Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees.
• Tree Puzzle - Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
• TreeMap - Experimental program for comparing host and parasite trees.
• TreeView - Simple program for displaying phylogenies.

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